The results of this work contribute to the understanding of the ecology of coral reefs in general. The development of the CaveCam provides the key for a new line of coral reef research allowing to explore and document the labyrinth of framework cavities interlacing coral reefs in a non-destructive way. It yields 1:1 close-up images of specimens up to 4 m inside the reef. Image analysis revealed a rich variety of mainly encrusting organisms. Coralline algae predominated on the walls near the cavity entrances, while darker inner sections of the cavities were colonized by a diverse cryptofauna: filter feeders abounded, notably sponges, which covered up to more than 50% of the substrate. Light is a crucial factor determining the balance between photoautotroph and heterotroph organisms near the cavity entrance, while food supply and competition for space shape the composition of the heterotroph community further away.With the newly developed LightSheet-method the complex morphology of the highly irregular framework cavities was described and reconstructed in 3-D, volume and wall area calculated.The metabolic activity of the coelobite communities is reflected in small-scale gradients in chlorophyll a and oxygen concentrations between cavities and freestream waters over the reef, where stronger gradients appear to be associated with reduced flow and higher coelobite cover. Direct and indirect measurements of water replacement rates within the cavities allowed first quantitative estimates of the bulk filtering effect of the coelobite community. We provide circumstantial evidence, that coelobite filter feeders are indeed causing the observed phytoplankton depletions of chlorophyll a and oxygen. Remineralization of the largely extrinsic organic matter taken up by the coelobite filter feeders may fuel close to 20% of the gross metabolism of the entire reef. A checklist of coelobite organisms in the Red Sea is provided.